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Overview of the formats developed by the Molecular Interactions Working Group and their relationships to other components in the community.
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The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception twenty years ago. Here we describe the general operation of the PSI, including its...
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Context 1
... PSI has developed numerous standardized data formats in the past 20 years and more are currently under development. An overview of the formats developed by the Molecular Interactions Working Group and their relationships to other components is summarized in Figure 1. The formats of the Mass Spectrometry Working Group and the Proteome Informatics Working Group and their relationships to other components are summarized in Figure 2. In this section we briefly describe each format, assess its current status, and provide links and citations for obtaining more information. ...
Citations
spectrum_utils is a Python package for mass spectrometry data processing and visualization. Since its introduction, spectrum_utils has grown into a fundamental software solution that powers various applications in proteomics and metabolomics, ranging from spectrum preprocessing prior to spectrum identification and machine learning applications to spectrum plotting from online data repositories and assisting data analysis tasks for dozens of other projects. Here, we present updates to spectrum_utils, which include new functionality to integrate mass spectrometry community data standards, enhanced mass spectral data processing, and unified mass spectral data visualization in Python. spectrum_utils is freely available as open source at https://github.com/bittremieux/spectrum_utils.
